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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtaaaacttatgtgatatggtcaatgatcaattgaccatgccataattcatgatgaagaattgtctgtgtgtttgatcaaattctgtatgtgattgggatagattgctgatcactgattcgtatatgacctcctttgagtattgacttcatttcttttgccttcatgggctttttcatttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTT

Basic information

species Glycine max
transcript GLYMA09G02270.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G02270.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G314679_T05 (Zea mays), 3'ss of exon 3
gtgtgtaaaacttatgtgatatggtcaatgatcaattgaccatgccataattcatgatgaagaattgtctgtgtgtttgatcaaattctgtatgtgattgggatagattgctgatcactgattcgtatatgacctcctttgagtattgacttcatttcttttgccttcatgggctttttcatttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTT
                                                                                  |  ||        | |||   | |  |  |  | | | | | |    || |  |  |  || | | | ||| |  ||  |||    ||    |||     ||  |||| || ||| || |||||||   | | ||||| |||||||||||||| || || |||||||| ||||| |||| ||| ||| |||| |||||||| |||||
----------------------------------------------------------------------------------aggttgatggcaaggttgaatttg--tattacttagtcactagggggtgtcgactctccagaaataaattc-tccctgatgc----atattttttgcttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATGACCTTCACTTTTTTGTCACCGCTGGAGATGATGAGAATGAGCTCATCTT

upper sequence: GLYMA09G02270.3 (Glycine max), 3'ss of exon 2
lower sequence: AT1G60970.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgtgtaaaacttatgtgatatggtcaatgatcaattgaccatgccataattcatgatgaagaattgtctgtgtgtttgatcaaattctgtatgtgattgggatagattgctgatcactgattcgtatatgacctcctttgagtattgact-tcatttcttttgccttcatgggctttttcatttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTT
                                                                          ||    |   |         || ||  ||||  |    |   |||  || |  |||  | |   |  | | ||  |  ||||| |  ||||          || || || ||  || |||| |  ||    | ||||| ||||||||||| ||||| ||||| |||||||| || ||||||||||| || |||||  | ||||| |||||||||||
--------------------------------------------------------------------------gtagatttcgacatcaaccatgttttagatacttcatagtgtacttgtt-gagtat--cttttatcaaatcttttccgtcattacaattgct-------agttcttgatatg-tagTGGAAGTGACAGCACTGGAGAACAACATTGTTGTGTACAAATTTGTGCAAGATCTCCATTTCTTTGTTACGGGCGGTGAAGAGGAAAACGAGCTTATCTT

upper sequence: GLYMA09G02270.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0003g02760.t01 (Vitis vinifera), 3'ss of exon 3
gtgtgtaaaacttatgtgatatggtcaatgatcaattgaccatgccataattcatgatgaagaattgtctgtgtgtttgatcaaattctgtatgtgattgggatagattgctgatcactgattcgtatatgacctcctttgagtattgacttcatttcttttgccttcatgggctttttcatttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTT
                                                                                | |||    |  |||| |  |  || | || | |    ||  |  |   ||     |||||| |   | |||   || ||||   ||  ||   |||||||| | |||||||| ||||||||||||||||| ||||||||||||||||| ||||||||||| ||||||||||||||||| ||||||||  |||||||||| || |||||
-------------------------------------------------------------------------------cttaaaactag--tgtggtgtgtttacaatgttcaaatttggct--tcactgctgctctttgaat---gccttgcctttttttttttttttg--ttttttcatct-acagCGGAGATAGCAATGTTTGAGAACAACATTGTTGTTTACAAATTTGTCCAAGACCTTCACTTCTTTGTTACTGGTGGTGAAGATGAAAATGAACTAATCTT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|192332965|gb|FK024614.1|FK024614
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCACACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|120493426|gb|EH221593.1|EH221593
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|120492487|gb|EH220654.1|EH220654
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|14259369|gb|BG882277.1|BG882277
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|298184953|gb|HO030166.1|HO030166
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGGCCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|151410972|gb|EV280787.1|EV280787
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|12689807|gb|BG156143.1|BG156143
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|151405407|gb|EV275221.1|EV275221
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|298191889|gb|HO035971.1|HO035971
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|151410188|gb|EV280003.1|EV280003
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|298186013|gb|HO031174.1|HO031174
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|19348506|gb|BM893038.1|BM893038
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|38192921|gb|CF922127.1|CF922127
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|213607061|gb|DB965059.1|DB965059
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|8670053|gb|BE191160.1|BE191160
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|14990780|gb|BI316453.1|BI316453
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|298178097|gb|HO027480.1|HO027480
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|298166245|gb|HO009216.1|HO009216
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|38192996|gb|CF922202.1|CF922202
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|298179376|gb|HO027847.1|HO027847
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|298182838|gb|HO031573.1|HO031573
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGGAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|14990797|gb|BI316470.1|BI316470
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|151406134|gb|EV275949.1|EV275949
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|192321195|gb|FK014285.1|FK014285
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|120532300|gb|EH260433.1|EH260433
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAN
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAA-
EST: gi|298170470|gb|HO019094.1|HO019094
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
EST: gi|298166774|gb|HO010213.1|HO010213
EST:     TGAGAAAGTTGTCTTCAACAAGACTCAGAAGGCCAGTGCCCGCACAGAAG                         CGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG
genomic: TGAGAAAGTTGTCTTCAACAAGACTCAGAAGACCAATGCCCGCACAGAAGgtgtgtaaaa ... catttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctttgagtattgacttcatttcttttgccttcatgggctttttcatttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTT
         tattgac  putative branch site (score: 2)
                                       ctttttcattt  putative PPT
                                        tttttcattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtaaaacttatgtgatatggtcaatgatcaattgaccatgccataattcatgatgaagaattgtctgtgtgtttgatcaaattctgtatgtgattgggatagattgctgatcactgattcgtatatgacctcctttgagtattgacttcatttcttttgccttcatgggctttttcatttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT